Hi, Thanks for the speedy fix! --Misha On Fri, 13 Aug 2010, Martin Morgan wrote: > On 8/13/2010 2:11 PM, Misha Kapushesky wrote: >> Hi, >> >> I put it on http://www.ebi.ac.uk/~ostolop/accepted_hits.sortednames.bam. >> After some more tinkering - it seems I can't reproduce this on my Mac, only >> on our Linux install. I also just noticed that the released version is >> 1.0.7, while we seem to have 1.1.11, and yet our R is 2.11.1 - perhaps it's >> a version incompatibility and we managed to install ourselves something >> incompatible? If that's the case, we'll probably try to get a more standard >> install going, and hopefully the problem will go away... >> > > This should be fixed in 1.0.8 (release) or 1.1.12 (devel), available via > biocLite in the next several days or via svn > (http://bioconductor.org/developers/source-control/) immediately. > > Thanks for the report and sample data. > > Martin > >> --Misha >> >> On Fri, 13 Aug 2010, Martin Morgan wrote: >> >>> Thanks Misha for the additional hints; I looked at the code and couldn't >>> see anything immediately wrong, but if you can provide a (minimal?) bam >>> file displaying the problem that would be helpful. Martin >>> >>> Misha Kapushesky <ostolop at="" ebi.ac.uk=""> writes: >>> >>>> Hi, >>>> >>>> I can add more detail to this - the same problem: >>>> >>>>> library( "Rsamtools" ) >>>> ... >>>>> tags <- c("NM", "MD", "XA", "XS","NS") >>>>> and_file = "SRR034792/tophat_out/accepted_hits.sortednames.bam" >>>>> and_bam = scanBam(and_file, param = ScanBamParam(flag = >>>>> scanBamFlag(isUnmappedQuery = FALSE), tag = tags)) >>>> >>>> *** caught segfault *** >>>> address 0x2b3449beb8cd, cause 'invalid permissions' >>>> >>>> Traceback: >>>> 1: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) >>>> 2: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = >>>> param) >>>> 3: scanBam(and_file, param = ScanBamParam(flag = >>>> scanBamFlag(isUnmappedQuery = FALSE), tag = tags)) >>>> 4: scanBam(and_file, param = ScanBamParam(flag = >>>> scanBamFlag(isUnmappedQuery = FALSE), tag = tags)) >>>> >>>> This error goes away if we don't include "XS" in tags, also if we use >>>> version 1.0.0 of Rsamtools. Any ideas? >>>> >>>> The sessionInfo() output is below. Thanks in advance! >>>> >>>> --Misha >>>> >>>>> sessionInfo() >>>> R version 2.11.1 (2010-05-31) >>>> x86_64-unknown-linux-gnu >>>> >>>> locale: >>>> [1] C >>>> >>>> attached base packages: >>>> [1] tools stats graphics grDevices utils datasets methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] Rsamtools_1.1.11 Biostrings_2.16.9 GenomicRanges_1.0.7 >>>> [4] IRanges_1.6.11 svMisc_0.9-57 JavaGD_0.5-2 >>>> [7] rJava_0.8-4 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] Biobase_2.8.0 >>>> >>>> >>>> On Thu, 12 Aug 2010, Andrew Tikhonov wrote: >>>> >>>>> Dear Biocore Team, >>>>> >>>>> We've got a problem where 'Rsamtools' produces segfaults and >>>>> core-dumps when reading a .bam file using the "XS" tag. We have a >>>>> faulty .bam and the list or R commands to reproduce it. Could you >>>>> please point us to someone who we may discuss this matter with and, >>>>> if possible, fix the problem. >>>>> >>>>> Thanks a lot in advance. >>>>> >>>>> Regards, >>>>> Andrew >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> -- >>> Martin Morgan >>> Computational Biology / Fred Hutchinson Cancer Research Center >>> 1100 Fairview Ave. N. >>> PO Box 19024 Seattle, WA 98109 >>> >>> Location: Arnold Building M1 B861 >>> Phone: (206) 667-2793 >>> >